Accelerating the development of model systems for marine microbial ecology through collaboration

113 Moore Foundation-supported co-authors from 53 institutions across 14 countries contributed to the Nature Methods article. All protocols in the article are openly available on protocols.io.

April 6, 2020

The oceans cover 70 percent of Earth’s surface and are home to an astonishing diversity of microbial life. Over the past 16 years, the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative has funded researchers around the world to identify marine microbes and learn how they interact with each other and the ocean environment. More than 100 of these scientists have published a compilation of protocols for performing genetics experiments on marine microbes as a resource article in the journal Nature Methods. The paper, entitled Genetic tool development in marine protists: emerging model organisms for experimental cell biology, is an essential step forward in understanding the cellular instructions that underpin microbial life in the sea.

A persistent bottleneck in microbial oceanography is the lack of experimental model systems – well-studied organisms that can be genetically manipulated to reveal gene function and expression as well as clarify how microbes contribute to ecosystem processes. One of our Marine Microbiology Initiative’s major funding strategies was a $15 million investment to support development of genetic tools for marine microeukaryotes (protists), among the most diverse yet least understood marine microbes.

Our experimental model systems portfolio offers a new way to catalyze genetic tool development in the marine microbial ecology research community.

The high-risk nature of the work and challenge to secure funding, specifically focused on tools, previously restricted scientists from making progress in this area. “A major limitation for the research I and other experimental model systems collaborators had previously was the lack of tools to genetically manipulate the diverse protists driving marine biogeochemical cycles and food webs,” said Dr. Jackie Collier, Associate Professor of Marine and Atmospheric Sciences at Stony Brook University. “It’s been very difficult to win funding from our typical sources to overcome that limitation because of the very high risk of failure inherent in such work. The Moore Foundation stepped in to take that risk, and that major investment has moved us individually and as a community onto a new frontier where we are poised to attack both old and new questions in new ways.”

Several research teams supported by the experimental model systems awards succeeded in introducing DNA into marine protists and are now working to employ genetic techniques, such as CRISPR/Cas9, to manipulate protist genomes. These efforts were accelerated by active communication and collaboration among the researchers, highlighted by over 200 laboratory protocols shared in a dedicated community group called Protist Research to Optimize Tools in Genetics (PROT-G) on the protocol-hosting website protocols.io.

Image: Abeoforma whisleri is a single-celled marine protist important in scientific research to understand the evolutionary origins of animals. In the above images, (A) An Abeoforma cell was (B) transformed with plasmid DNA encoding a fluorescence protein to (C) label A.whisleri nuclei, enabling an experimental model systems team to better study the life cycle of this organism.

Global collaboration + open access

The Nature Methods article brings together 113 Moore Foundation-supported co-authors from 53 institutions across 14 countries and offers instructions and a wide selection of protocols for conducting genetics in marine protists. All protocols in the article are openly available on protocols.io to help other scientists benefit from this effort.

“This paper is a landmark achievement by the experimental model systems grantees after several years of hard work to solve numerous technical challenges in the laboratory,” said Adam Jones, Ph.D., program officer at the Gordon and Betty Moore Foundation. “We look forward to seeing how the protocols and guidance offered by the scientists in this newly available resource accelerate genetic tool development in marine protists. We admire their efforts and consider this paper a great way to help celebrate the conclusion of the Marine Microbiology Initiative.”